I'm the same. I use both, but I do like cia for some things. I kinda filter it in my mind what I want as a cia and as a .3dsx, but for me, generally, all tools (D9, Ftp, etc) are gonna be homebrew applications while game related stuff (Pchex++, JK's SaveManager) are cias. That's just me though and it's kinda weird.